I am a pilot not a doctor, so, unqualified opinion.
If the knee is being forced apart by debris, the ligaments will hurt in the short term, and become inflamed in the medium to long term. It is a close tolerance joint, and it doesn't take much.
It is vital to get a definite answer to the problem, and I feel that MRI or visual probing optically is the only way forward. X-rays do not show some of the possible culprits.
If you want to keep the thread going, I'll try to be a little more detailed when time permits.